The Himalayan–Tibetan Orogeny, driven by the convergence of the Indian and Eurasian plates, has resulted in significant crustal thickening, intense deformation and widespread magmatism. This tectonic collision has generated deep-seated faults and shear zones that facilitates fluid circulation and heat transfer, leading to the formation of numerous hydrothermal systems in the region. While Tibetan geothermal systems are largely mantle-derived, the origin of hot springs, geothermal fluids and heat flow in Indus River Basin remained debated. Understanding the sources of solutes, volatiles and heat is significant for constraining the tectonic and geothermal evolution of the region. This study integrates geochemical, geological and geophysical data to examine heat flow and fluid circulation in geothermal systems of Indus River Basin. High concentration of major ions, trace elements and rare alkali metals (Arsenic, Cesium and Lithium) in Puga–Chumathang springs indicate fluid contribution from crystallizing magma from the shallow to mid-crust. Crustal helium and carbon isotopic signatures further supports crustal magmatic influence, particularly near the Indus Suture Zone. Estimated reservoir temperatures of 205–290 °C and circulation depths of ~ 4000 m suggesting a localized heat source in the region. Geophysical evidences, including negative gravity anomalies and low-resistivity zones beneath the ISZ, also indicated the presence of partially molten material in the shallow to mid-crust. These anomalies, combined with minimal seismic activity, highlight zones of high heat flow and active fluid migration pathways. Our findings suggest that partial melting, driven by reduced lithostatic pressure and crustal decompression, enhances geothermal activity. This study provides new insights into the geothermal evolution of the Himalayan–Tibetan Orogenic Belt, emphasizing crustal processes in sustaining high-temperature hydrothermal systems. The results have significant implications for geothermal resource assessment and sustainable energy development, revealing the complex interplay of magmatic, tectonic and hydrothermal processes in shaping these systems.